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Fig. 4 | Genome Biology

Fig. 4

From: A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

Fig. 4

Proteomics analysis suggests a role for TRAM2 in YAP-induced EMT. a Volcano plots of the proteomics studies in MCF10A cells transduced with the indicated vectors. The data was compared and normalized to control cells. Dark dots are the proteins that were significantly upregulated or downregulated compered to control using a cutoff of absolute LFC > 0.5 and adjusted p value < 0.05. YAP is labeled green and TRAM2 blue. b Venn diagrams representing the significant overlap of upregulated (Fisher’s exact test p value 4.09E−27) or downregulated (Fisher’s exact test p value 6.11E−19) proteins between YAP and TRAM2 samples compared with control in a. c Bubble plot summarizing gene set enrichment analysis from the proteomics data presented in a. Significantly enriched gene sets (FDR < 0.25) in at least one condition were selected, and the normalized enriched scores were plotted for both samples. Bubble sizes represent the number of genes in each gene set, while the fill colors represent the FDR values as indicated. d GSEA plots of the EMT-hallmark molecular signature using the proteomics data described in a. e Volcano plots of proteomics studies in MCF10A-YAP5SA cells transduced with the indicated vectors. The data was compared and normalized to control cells (non-targeting sgRNA). Dark dots are the proteins that were significantly upregulated or downregulated compered to control with cutoff of absolute LFC > 0.5 and adjusted p value < 0.05. f Venn diagrams representing the overlap of upregulated (Fisher’s exact test p value 6.00E−07) or downregulated (Fisher’s exact test p value 2.01E−30) proteins between TRAM2-KO1 and TRAM2-KO2 samples compared with control samples in the proteomics studies presented in e. g Bubble plot represents a gene set enrichment analysis from the proteomics data presented in e. Significantly enriched gene sets (FDR < 0.25) in at least one condition were selected, and the normalized enriched scores were plotted for both samples. Bubble sizes represent the number of genes in each gene set, while the fill colors represent the FDR values as indicated. h GSEA plots of the EMT-hallmark molecular signature using the proteomics data described in e

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